Maybe within the snapshotting event set the size of the layout and scroll to the part of the screen you want to screenshot of, snapshot, and then immediately set the screen back to the prior settings. Never tried if that works, but that's the only approach I can think off with the standard objects of Construct 2 for now.

I haven't done it in a long time, but I think MindfaQ's method is how I did it. Set everything but what you want invisible, including the background layer if you want transparent PNGs. I think it flashed on screen for one tick, but you hardly noticed it happen.